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- PDB-4fre: Crystal Structure of BBBB+UDP+Gal at pH 6.5 with MPD as the cryop... -

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Basic information

Entry
Database: PDB / ID: 4fre
TitleCrystal Structure of BBBB+UDP+Gal at pH 6.5 with MPD as the cryoprotectant
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / MANGANESE / ABO ROSSMANN FOLD / RETAINING GLYCOSYLTRANSFERASE / GLYCOPROTEIN / BLOOD GROUP ANTIGEN / METAL-BINDING
Function / homology
Function and homology information


fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding ...fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region / membrane / metal ion binding
Similarity search - Function
Glycosyl transferase, family 6 / Glycosyltransferase family 6 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranose / DI(HYDROXYETHYL)ETHER / URIDINE-5'-DIPHOSPHATE / Histo-blood group ABO system transferase / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsJohal, A.R. / Alfaro, J.A. / Blackler, R.J. / Schuman, B. / Borisova, S.N. / Evans, S.V.
CitationJournal: Glycobiology / Year: 2014
Title: pH-induced conformational changes in human ABO(H) blood group glycosyltransferases confirm the importance of electrostatic interactions in the formation of the semi-closed state.
Authors: Johal, A.R. / Blackler, R.J. / Alfaro, J.A. / Schuman, B. / Borisova, S. / Evans, S.V.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7394
Polymers34,0481
Non-polymers6903
Water3,351186
1
A: Histo-blood group ABO system transferase
hetero molecules

A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4778
Polymers68,0972
Non-polymers1,3816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5920 Å2
ΔGint-22 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.296, 150.809, 79.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-646-

HOH

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Components

#1: Protein Histo-blood group ABO system transferase


Mass: 34048.262 Da / Num. of mol.: 1 / Fragment: GTB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Plasmid: PCW DELTA 1AC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD
References: UniProt: H6A2X0, UniProt: P16442*PLUS, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ELECTRON DENSITY FOR RESIDUE 195 IS CONSISTENT WITH GLY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1% PEG 4000, 5% MPD, 5 mM manganese chloride, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM ADA, 30 mM sodium acetate with 20% MPD as cryoprotectant, pH 6.5, VAPOR DIFFUSION, HANGING ...Details: 1% PEG 4000, 5% MPD, 5 mM manganese chloride, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM ADA, 30 mM sodium acetate with 20% MPD as cryoprotectant, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 26, 2012 / Details: 9 CCDs, 9 TILED FIBER-OPTIC TAPERS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 26912 / % possible obs: 98.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-1.885.80.313197.7
1.88-1.925.80.264199.5
1.92-1.955.80.228198.1
1.95-1.995.70.213199.6
1.99-2.045.80.185198.1
2.04-2.085.70.166199.1
2.08-2.145.70.153199.3
2.14-2.195.70.14198.4
2.19-2.265.60.129199.9
2.26-2.335.50.115198.7
2.33-2.415.40.112198.5
2.41-2.515.40.105199
2.51-2.625.30.096199
2.62-2.765.30.087199.4
2.76-2.945.20.08199.1
2.94-3.165.10.073199.3
3.16-3.484.90.066198.8
3.48-3.984.80.06198.1
3.98-5.024.80.056198.4
5.02-404.60.056196.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.24 Å
Translation2.5 Å36.24 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SXG

3sxg


Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.635 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22201 1350 5 %RANDOM
Rwork0.18748 ---
obs0.18921 25525 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 44 186 2386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022267
X-RAY DIFFRACTIONr_bond_other_d0.0010.021556
X-RAY DIFFRACTIONr_angle_refined_deg2.0181.9723079
X-RAY DIFFRACTIONr_angle_other_deg1.093.0013742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53322.71107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8915372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7321518
X-RAY DIFFRACTIONr_chiral_restr0.1280.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 93 -
Rwork0.229 1696 -
obs--96.29 %

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